rs137852895
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_024312.5(GNPTAB):c.1220A>G(p.Asp407Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D407A) has been classified as Pathogenic.
Frequency
Consequence
NM_024312.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.1220A>G | p.Asp407Gly | missense_variant | 10/21 | ENST00000299314.12 | |
GNPTAB | XM_011538731.3 | c.1139A>G | p.Asp380Gly | missense_variant | 10/21 | ||
GNPTAB | XM_006719593.4 | c.1220A>G | p.Asp407Gly | missense_variant | 10/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.1220A>G | p.Asp407Gly | missense_variant | 10/21 | 1 | NM_024312.5 | P1 | |
GNPTAB | ENST00000549940.5 | c.1220A>G | p.Asp407Gly | missense_variant | 10/11 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at